I've noticed this on Last Stand and Fort Zulu mostly; some maps will run just fine and others will lag insanely. It's the difference between "Incredibly smooth" and "If I time this just right, I'll be able to click on my unit!"

Am running Windows XP on a Dell Dimension 8250 with an NVIDIA Geforce 6800 GT. Once again, there are lots of maps I can play just fine, but a few of them have horrible lag.

EDIT: On closer inspection, it's a gradual thing. I went into single-player to test this, and it starts off fairly smooth but then the lag steadily increases from the time I start playing one of these maps. Switching from Fort Zulu to Last Stand had no effect; the FPS starts off about where it was and then drops steadily. Switching to Field Of Unending Dawn instantly reverts it to perfect normality.

Maps with laser fences are, for some reason, more intensive than maps without them (that is going to account for some of the lag). Also, as more DGs enter the field, and more souls are being kept track of, more work needs to be done per frame. You can reduce the lag to some extent by turning down the settings, and by not looking at areas that are causing lag (i.e. large patches of souls, or laser fences). About all I can do is tell you to learn to live with it, and don't play maps that cause problems, though I am sure that someone who knows more about your video card might be able to offer other advice (such as: upgrade).